A Linear-Time Parameterized Algorithm for Computing the Width of a DAG

Cáceres, Manuel; Cairo, Massimo; Mumey, Brendan; Rizzi, Roméo; Tomescu, Alexandru I.

doi:10.1007/978-3-030-86838-3_20

Cited by 1 publication

(1 citation statement)

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“…We extracted subgraphs of different sizes of the LRC variation graph and run the optimized and unoptimized versions of our algorithm. Sugraphs were taken as subgraphs induced by a consecutive segment of vertices in a topological order, which guarantees the width of the resulting subgraph to be at most the width of the original graph [75].…”

Section: Choice Of Parameter and Its Effect On Correctnessmentioning

confidence: 99%

Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG

Cáceres¹,

Mumey²,

Husić³

et al. 2022

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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A multi-assembly problem asks to reconstruct multiple genomic sequences from mixed reads sequenced from all of them. Standard formulations of such problems model a solution as a path cover in a directed acyclic graph, namely a set of paths that together cover all vertices of the graph. Since multi-assembly problems admit multiple solutions in practice, we consider an approach commonly used in standard genome assembly: output only partial solutions (contigs, or safe paths), that appear in all path cover solutions. We study constrained path covers, a restriction on the path cover solution that incorporate practical constraints arising in multi-assembly problems. We give efficient algorithms finding all maximal safe paths for constrained path covers. We compute the safe paths of splicing graphs constructed from transcript annotations of different species. Our algorithms run in less than 15 seconds per species and report RNA contigs that are over 99% precise and are up to 8 times longer than unitigs. Moreover, RNA contigs cover over 70% of the transcripts and their coding sequences in most cases. With their increased length to unitigs, high precision, and fast construction time, maximal safe paths can provide a better base set of sequences for transcript assembly programs.

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Section: Choice Of Parameter and Its Effect On Correctnessmentioning

confidence: 99%